Literature DB >> 30679593

Process calculi may reveal the equivalence lying at the heart of RNA and proteins.

Stefano Maestri1, Emanuela Merelli2.   

Abstract

The successful use of process calculi to specify behavioural models allows us to compare RNA and protein folding processes from a new perspective. We model the folding processes as behaviours resulting from the interactions that nucleotides and amino acids (the elementary units that compose RNAs and proteins respectively) perform on their linear sequences. This approach is intended to provide new knowledge about the studied systems without strictly relying on empirical data. By applying Milner's CCS process algebra to highlight the distinguishing features of the two folding processes, we discovered an abstraction level at which they show behavioural equivalences. We believe that this result could be interpreted as a clue in favour of the highly-debated RNA World theory, according to which, in the early stages of cell evolution, RNA molecules played most of the functional and structural roles carried out today by proteins.

Entities:  

Year:  2019        PMID: 30679593      PMCID: PMC6345955          DOI: 10.1038/s41598-018-36965-1

Source DB:  PubMed          Journal:  Sci Rep        ISSN: 2045-2322            Impact factor:   4.379


  7 in total

1.  Database of non-canonical base pairs found in known RNA structures.

Authors:  U Nagaswamy; N Voss; Z Zhang; G E Fox
Journal:  Nucleic Acids Res       Date:  2000-01-01       Impact factor: 16.971

Review 2.  Protein misfolding and human disease.

Authors:  Niels Gregersen; Peter Bross; Søren Vang; Jane H Christensen
Journal:  Annu Rev Genomics Hum Genet       Date:  2006       Impact factor: 8.929

Review 3.  Molecular chaperones in protein folding and proteostasis.

Authors:  F Ulrich Hartl; Andreas Bracher; Manajit Hayer-Hartl
Journal:  Nature       Date:  2011-07-20       Impact factor: 49.962

4.  How Does Mg2+ Modulate the RNA Folding Mechanism: A Case Study of the G:C W:W Trans Basepair.

Authors:  Antarip Halder; Rohit Roy; Dhananjay Bhattacharyya; Abhijit Mitra
Journal:  Biophys J       Date:  2017-05-12       Impact factor: 4.033

5.  Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution.

Authors:  D Allan Drummond; Claus O Wilke
Journal:  Cell       Date:  2008-07-25       Impact factor: 41.582

6.  Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions.

Authors:  Matthew W Powner; Béatrice Gerland; John D Sutherland
Journal:  Nature       Date:  2009-05-14       Impact factor: 49.962

7.  Topology driven modeling: the IS metaphor.

Authors:  Emanuela Merelli; Marco Pettini; Mario Rasetti
Journal:  Nat Comput       Date:  2015       Impact factor: 1.690

  7 in total
  2 in total

1.  RNA secondary structure factorization in prime tangles.

Authors:  Daniele Marchei; Emanuela Merelli
Journal:  BMC Bioinformatics       Date:  2022-08-18       Impact factor: 3.307

2.  Structural relation matching: an algorithm to identify structural patterns into RNAs and their interactions.

Authors:  Michela Quadrini
Journal:  J Integr Bioinform       Date:  2021-05-31
  2 in total

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